The JFA Institute includes experts in program evaluations. The program evaluation team has well developed methodologies to conduct organizational assessments of correctional and other justice agencies. Typically, evaluations include an examination of the strength and weakness of an organization. Areas reviewed include: organizational structure and leadership, organizational processes, personnel policies and training, diagnosis processes, collaboration approaches, information systems, and quality control strategies (performance and outcome measures).

Recent major program evaluations conducted include the evaluation of the Texas system of prosecuting parental rights termination cases; an organizational assessment of the probation department in Travis County (Austin, Texas); and, an assessment of the prison rape prevention program in Texas prisons sponsored by the National Institute of Justice, U.S. Department of Justice. The Institute has also completed studies of boot camp programs (adult and juvenile), residential substance abuse programs, electronic monitoring programs, and assessed a variety of alternatives to incarceration policy initiatives.